3 sort of problems were reported:
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1) Model error: non-tag ?Journal in column in model ?Paper
//------------------------------------------------------------------
?Journal Paper ?Paper XREF Journal
//------------------------------------------------------------------
?Paper Reference Title UNIQUE ?Text
Journal UNIQUE ?Journal XREF Paper
Unpublished
Journal does, in fact appear as a tag in tags.wrm.
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First of all, tags.wrm can be removed before constructing
a new database,
the file must stay if the database was constructed before 3.3
but really this does not apply to ace4 databases
also the construction:
Journal UNIQUE ?Journal XREF Paper
Unpublished
is not legal
in a given column one should not mix up tags and class objects
the corerect model should say
?Paper Reference Title UNIQUE ?Text
J UNIQUE Journal ?Journal XREF Paper
Unpublished
in fact it is closer to real life
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2) Model error: tag Strain outside rooted subtree in model ?DNA_Sample
//------------------------------------------------------------------
?DNA_Sample Genomic ?Species Strain Text
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This is indeed illegal
only basic or constructed types may appear to the right of a pointer
you should say
?DNA_Sample Genomic ?Species #St
#St Strain Text
or you can have
?DNA_Sample Genomic ?Species ?Strain
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3) Model error: In model ?Library, tag Paper XREF's to tag Library
in class ?Paper
can't find tag Library in model ?Paper
//------------------------------------------------------------------
?Library Name Text // Full name
Description ?Text // Description of material included
Laboratory ?Laboratory
Author ?Author
Paper ?Paper XREF Library
Experiment ?Experiment XREF Library REPEAT
Donor_Species ?Species
Strain Text
Library_Type UNIQUE cDNA
Genomic UNIQUE sheared
Restriction_Enzyme Text
Vector ?Vector
Restriction_Site Text Text
Host_Strain ?Bacterial_Stock
very true: you are trying to XREF to a non existing tag
this is clearly a bug
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The fatsest way to edit the models is to open emacs
edit the models file
and in a separate window to start tace and issue the command
read_model
this is much better for that task than using xace
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ace 4 models support DateType , look in the session object to see
the date foramt
correect dates are for example
now
today
1996
1992-01-25
1995-01-25_18:11:37
..
in addition the coming 4.2 supports COORD modificator inside
sequence models to indicate numbers which may slide when an
insertion is made
say i insert a base in 200
then internally the code will edit every COORD > 200 to
increase by 1
there is no esxternal interface yet for this thing but it
is used by our sequence manipulation tools
Jean